Show genes annotated with a specified GO term. Optionally constrain the organism and the evidence code. (Includes 'with' annotation: the 'with' field holds an additional identifier for annotations using certain evidence codes)

Find all genes that are associated with a particular GO term in a specific organism. This template will return genes that have been assigned the given GO term as well as genes that have a more specific GO term.

For specified D. melanogaster transcription factor(s), show the binding sites, chromosomal locations, genes where the sites are located and give the sequence of the binding site, if any. (Data Source: Redfly).

Show all known regulatory elements for a particular D. melanogaster gene. Regulatory elements can include: CRMs and TF binding sites from REDfly and enhancers from FlyBase. (Data Source: REDfly, FlyBase).

For a given Gene (or List of Genes) in named organism (default: D. melanogaster) returns the orthologues and the sequence of the gene(s) and orthologous genes. Optionally constrain the organism for which orthologues are shown and the data source from which the orthologue predictions are derived. Currently orthologue predictions are available from TreeFam, Panther and the Drosophila 12 genomes project. [keywords: homologue, homolog, paralogue, paralogue, ortholog]

For a particular Drosophila gene show results from Arbeitman et al (2002) microarray time course expression. Optionally constrain by a specific stage and filter on the median signal ratio. Note that the reference sample in this experiment is pooled mRNA representing all stages of the life cycle. To query general stages change = to LIKE and enter e.g. *Embryo* or *Adult*.

For a particular gene, show any regulatory elements found in its upstream intergenic region and the chromosome location of these regions. Regulatory elements can include: CRMs and TF binding sites from REDfly and enhancers from FlyBase. (Data Source: REDfly, FlyBase).

For a given Gene (or List of Genes) in named organism (default: D. melanogaster) returns the orthologues. Optionally constrain the organism for which orthologues are shown and the data source from which the orthologue predictions are derived. Currently orthologue predictions are available from TreeFam, Panther and the Drosophila 12 genomes project. [keywords: homologue, homolog, paralogue, paralogue, ortholog]

Show gene expression data for a particular developmental stage according to the Arbeitman et al data set and filter this data on the median signal ratio. This template allows you to query on the general stage: use LIKE *Embryo*; *Larvae*; *Metamorphosis*; *Adult female* or *Adult male*. The templates Microarray Time course data from Arbeitman et al (filter on specific stage (and ratio)) --> Genes [D. melanogaster], allow you to filter on more specific stages. Note that the reference sample in this experiment is pooled mRNA representing all stages of the life cycle.

For a given gene or set of genes show orthologous human genes which have an associated OMIM disease. Optionally constrain the search to use a particular orthologue mapping (Ensembl Compara or TreeFam).

Given a gene show the associated GO terms, and all parents to the top of the directed graph. The query returns a column containing the assigned GO term and a column containing all parents of that primary assignment.

Show genes expressed in a set of tissues/stages according to the modENCODE RNA_seq data. The expression scores are binned into the expression levels as follows: No/Extremely low expression: 0-0; Very low expression: 1-3; Low expression: 4-10; Moderate expression: 11-25; Moderately high expression: 26-50; High expression: 51-100; Very high expression: 101-1000; Extremely high expression: >1000;

For a specified gene or list of genes show the alleles and the stocks available. Optionally, you can filter the search with a specific allele of the gene and/or show only those stocks available from a specified stock centre.

Show all the genes known to be involved in a specific KEGG, REACTOME or FlyReactome pathway and their orthologous genes in one specific organism. (Data Source: KEGG, Reactome, FlyReactome, inParanoid, Drosophila consortium).

For a specific chromosomal location of D. melanogaster, show all CRMs and the TF binding sites that overlap these CRMs, according to REDfly. Show the chromosomal positions and lengths of all CRMs and TF binding sites.

Show all D. melanogaster genes that have been annotated with a particular GO term and the DrosDel deletions which would delete these genes. Show whether the deletion is available. (Data Source: GO, FlyBase, DrosDel).

Show the CDS and its sequence for all genes from a particular organism. This template contains an additional constraint to limit the result to one CDS per sequence (e.g all -PA CDS from D. melanogaster).

For a particular A. gambiae gene, show its expression according to the data of Koutsos et al at a particular developmental stage. This template allows you to query on the general stage: use LIKE embryo; larva; pupa; adult female; adult male; or adult. The templates Gene [A. gambiae] -> Life cycle expression data (filter on specific stage (and ratio)) allow you to filter on more specific stages. Note that the reference sample in this experiment is pooled RNA produced in vitro from ESTs that were used as substrates to produce amplicons for the spotted microarrays.

For the following intergenic region from D. melanogaster, show all regulatory elements with their chromosomal locations and lengths. Regulatory elements can include: CRMs and TF binding sites from REDfly, enhancers from FlyBase and predicted sites from Tiffin. (Data Source: FlyBase, REDfly, Tiffin).

This search returns the publications referenced by Uniprot AND the publications for the Gene. This gives two columns of pubmed Ids: the first for the publications from Uniprot and the second for the publications for the Gene. To create a single list of all publications, create a list for the first set and then add the second set to this list using the functions under 'Create/Add to list'.